File naming and size

All the software in the QUINT workflow have requirements for the input images:

  • The file naming convention applies to all the software. It is recommended to change the file names as the first step in the QUINT workflow. This ensures that the files are compatible with QuickNII and VisuAlign, and that the output files of QuickNII, VisuAlign and ilastik are directly compatible with Nutil.

  • As the image size requirements for QuickNII and Ilastik differ, it is recommended to create two image series that comply with their respective requirements.

Tip

The Nutil software can be used to prepare the images since it supports image transformations (downscaling, rotation, mirroring), file renaming and file format conversion. Alternative software such as FIJI or Adobe Photoshop can also be used.

Naming convention

  • Add a unique ID to the file names of the images reflecting the serial order and spacing of the sections. The format is: _sXXX with XXX representing the section number (not restricted to three digits). As QuickNII propagates the registration using these numbers, it is important they respect the order and spacing (in case of coronal sections, can be either from anterior to posterior or posterior to anterior).

  • Do not use periods “.” or spaces (” “) in the file name. This will not work.

  • As Nutil scans and detects the “_s” part of the name, the file name must not contain additional “_s” (for example “tg2345_MMSH_ss_s001.png” will not work).

Example for consecutive sections: _s0001, _s0002, _s0003. Example for every fourth section starting with the third section: _s003, _s007, _s0011.

_images/NamingConvention.PNG

Tip

The Quantifier feature in Nutil uses the unique IDs to match up corresponding atlas maps, segmentations and registration information in the JSON file from QuickNII/VisuAlign. While not recommended, it is possible to bypass the naming convention in Nutil using Regular Expressions (RegExp) as long as there is a consistent naming convention across the files. For more information see the “Help” button in the Nutil GUI or contact user support.